Magneto captured the X-Men one by one, with only the Iceman remaining uncaptured, but he is in critical condition in the hospital. Magneto has placed the X-Men in a large metallic sphere which is send towards space with an air balloon. Once the sphere reaches space, the X-Men will suffocate.
As Magneto celebrates his victory he makes the Xavier's school as his new Headquarters, destroying all equipment that he doesn't need himself, which includes Cerebro. When the parents of the Angel arrive at the school for a visit, he opens the door for them and then uses magnetic attraction to put them under his control. He then suggests that they are very tired and sends them to a guest room upstairs to get some sleep; the Worthingtons do as told.
At the hospital Iceman is still in critical condition and delirious. Dr. Thomas, who has been taking care of him, tries a new experimental sulfa drug, but to inject it through his body’s icy exterior he needs to apply it with a laser induced hypodermic. The drug has an immediate effect and Iceman finally quiets down. Both nurse and doctor hope that Iceman is now on the way to recovery.
Meanwhile in the balloon the X-Men are still unconscious. The professor is awake, but because of a mental-wave disruptor attached to his head he can't use his powers. He tries to stress and strain the disruptor with all the power he has until the device explodes and Xavier is free again.
Once free, Xavier checks on his students and he mentally wakes the unconscious X-Men. They try to think of a way to escape from the balloon, as they are already too high, and if Cyclops blasts a hole into their prison, their remaining oxygen will get sucked out in seconds.
Meanwhile Magneto came up with an evil plan. He rearranges lots of Xavier’s equipment and by duplicating the body cells of Angel's parents he wants to create an army of mutants.
In the balloon the professor orders Marvel Girl to try and push them telekinetically downwards again, At the same time he uses his power to locate Magneto and tries to see what he is up to. He learns of Magneto's plan and the team decides that Iceman is their only hope now.
The professor succeeded in contacting and awakening Bobby at the hospital; the sulfa drug has helped Iceman but he is still very weak, yet he is needed. Iceman gets up and leaves the hospital through a window by creating himself an ice slide.
Marvel Girl has succeeded in stop the balloon from rising, however she is not powerful enough to push it downwards to earth. Xavier tells her that she shall keep them steady, while he once more probes Magneto’s mind, to learn how he escaped from the Stranger.
Magneto and Toad are on a strange deserted planet where they are the prisoners of the Stranger. They are allowed to move around freely on the planet since the Stranger doesn't expect them to be able to escape.
Magneto and Toad find some old ships in some sort of museum. While the Stranger is gone, surveying other worlds, Magneto uses an iron gate and forms it into a ladder, boarding one of the old ships. He uses his magnetic powers to operate the ship, but he first kicks out the Toad since he is no longer of any use to him. Thus Magneto managed to escape from the Stranger.
Bobby arrives at the school and investigates the place while Magneto created a machine to duplicate the body cells of Angel's parents. As the machine operates several forms are created in tubular containers that resemble humanoids. But suddenly something interferes with the
duplication process because the Iceman has created an ice barrier on top of the sleeping parents of Angel. Because of this barrier the body cells can't be extracted from them.
As soon as Magneto finds out something is wrong with the machine he suspects Iceman’s involvements and finally finds him in the bedroom with Angel's parents. He immediatly throws every metallic object in the room towards Iceman, but he manages to get out on an ice sled, through an ice tunnel.
Magneto enters the ice tunnel going after Iceman, but he doesn't realize that Iceman set up a trap while Magneto was working on his body cell machine. The ice tunnel is connected to a large ice igloo just outside of the school which now contains both the Iceman and Magneto. Bobby's plan was to get out of an opening he prepared as soon as Magneto was there, but Magneto quickly closes the hole in the igloo magneticly, which puts Iceman in a tough position since he is still too weak to fight Magneto.
In the meantime the professor was monitoring Iceman and realizes that he must do something quickly before Iceman is history. He makes Cyclops create several small holes in the balloon so the gas in it can escape, and the balloon sinks back down to the ground. Because the balloon descends too fast, Jean has to use her power to slow down their fall. Once the balloon safely lands, Scott blasts the metal sphere so they can escape. The professor sends the team towards Bobby to help him and create a diversion.
Since the balloon landed in the same place where it was launched, the team arrives quickly near the icedome that Iceman created. Scott blasts a hole in it and the X-Men fight Magneto.
Magneto doesn't want to risk anything and threatens to kill the Iceman if the others don't stop fighting immediatly, but Angel dives in and manages to lift Iceman back to safety. The battle continues until the professor yells to stop the fight.
While the team created a diversion the professor stayed at the sidelines to concentrate his power. He contacted the Stranger who is on his way back to earth to recapture Magneto as his trophy. Magneto wants to prevent being captured again and quickly flees in his magna-car, with the Stranger hot on his trail.
Next the team destroys Magneto's machine before any mutants have emerged from it.
The next morning the Warren’s parents wake up, not remembering anything and the X-Men can finally relax for a change.